All Resources

Resources

Below you can find tutorials, selected datasets and documentation to help you use the tools and services EBRAINS offers. To find software and other digital tools, please refer to the dedicated tools page. Scientific publications may be found on the publications page. In the EBRAINS Knowledge Graph you can search all datasets and models.

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WHS rat brain atlas v1.01 (Papp et al., 2015)

The main focus of our original article was to describe the anatomical delineations constituting the first version of the WHS Sprague Dawley atlas, apply the Waxholm Space coordinate system, and publish the associated MRI/DTI template and segmentation volume in their original format. To increase usability of the dataset, we have recently shared an updated version of the volumetric image material (v1.01). The aims of this addendum are to inform about the improvements in the updated dataset, in particular related to navigation in the WHS coordinate system, and provide guidance for transforming coordinates acquired in the first version of the atlas.

WHS rat brain atlas v1 (Papp et al., 2014)

Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI.

Exploring EBRAINS brain atlases using siibra-explorer

Exploring the EBRAINS brain atlases using the siibra-explorer, an interactive online 3D atlas viewer, and learning how the human brain atlas is structured.

Data Curation Collab

The aim of this collab is to provide you with all the information you need to publish your neuroscience data via the EBRAINS Knowledge Graph.

Building and simulating a simple model using PyNN

In this tutorial, you will learn how to build a simple network of integrate-and-fire neurons using PyNN, how to run simulation experiments with this network using different simulators, and how to visualize the data generated by these experiments.

Finding data in EBRAINS

This video shows you how to find a neuroscience dataset in the EBRAINS Knowledge Graph.

Preparing your data - The data descriptor

This video discusses the importance of providing a data descriptor alongside your data and gives advice on how to prepare such a document for the purpose of sharing data through EBRAINS.

Preparing your data - Metadata organisation

This video gives an introduction to the importance and benefits of metadata organisation for a neuroscience researcher. It then explains how EBRAINS organises and integrates metadata to provide an easy and user-friendly service.

Preparing your data - Data organisation

This video outlines the importance of data organisation and best practices.

What is open data and EBRAINS data sharing?

This video gives an overview of open data and how to share data on EBRAINS.

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